Paying your fees does not file your tax return. You have to go all the way through the FILE section and e-file your returns yourself. If you filed your federal but waited for state for some reason, it was still up to you to go back and e-file those returns. It is too late now to e-file past year returns, so they will need to be filed by mail. Print, sign and date them, and mail them to the state.
Or....did you not even prepare the non-resident CA returns? Do you still need to prepare them? This may be a problem if you already prepared and filed resident state returns for those years, since you are supposed to prepare the non-resident state return first--before you prepare a return for the state you lived in. What state did you live in for those years?